def main(): #main_dir = dirname(__file__) args = docopt(__doc__) fasta_f = args['--infile'] fasta_type = args['--type'] sam_fs = args['--sam'] bam_fs = args['--bam'] cov_fs = args['--cov'] cas_fs = args['--cas'] hit_fs = args['--hitsfile'] prefix = args['--out'] nodesDB_f = args['--db'] names_f = args['--names'] nodes_f = args['--nodes'] taxrules = args['--taxrule'] min_bitscore_diff = float(args['--min_diff']) tax_collision_random = args['--tax_collision_random'] title = args['--title'] # outfile out_f = BtIO.getOutFile("blobDB", prefix, "json") if not (title): title = out_f # coverage if not (fasta_type) and not bam_fs and not sam_fs and not cov_fs and not cas_fs: BtLog.error('1') cov_libs = [BtCore.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \ [BtCore.CovLibObj('sam' + str(idx), 'sam', lib_f) for idx, lib_f in enumerate(sam_fs)] + \ [BtCore.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)] + \ [BtCore.CovLibObj('cov' + str(idx), 'cov', lib_f) for idx, lib_f in enumerate(cov_fs)] # taxonomy hit_libs = [BtCore.HitLibObj('tax' + str(idx), 'tax', lib_f) for idx, lib_f in enumerate(hit_fs)] # Create BlobDB object blobDb = BtCore.BlobDb(title) blobDb.version = blobtools.__version__ # Parse FASTA blobDb.parseFasta(fasta_f, fasta_type) # Parse nodesDB OR names.dmp, nodes.dmp nodesDB_default = join(blobtools.DATADIR, "nodesDB.txt") nodesDB, nodesDB_f = BtIO.parseNodesDB(nodes=nodes_f, names=names_f, nodesDB=nodesDB_f, nodesDBdefault=nodesDB_default) blobDb.nodesDB_f = nodesDB_f # Parse similarity hits if (hit_libs): blobDb.parseHits(hit_libs) blobDb.computeTaxonomy(taxrules, nodesDB, min_bitscore_diff, tax_collision_random) else: print BtLog.warn_d['0'] # Parse coverage blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=None) # Generating BlobDB and writing to file print BtLog.status_d['7'] % out_f BtIO.writeJson(blobDb.dump(), out_f)
def output(self): # meta meta = self.get_meta() meta_f = join(self.view_dir, "meta.json") BtIO.writeJson(meta, meta_f, indent=2) # gc gc_f = join(self.view_dir, "gc.json") print BtLog.status_d["13"] % (gc_f) BtIO.writeJson(self.gc, gc_f, indent=1) # length length_f = join(self.view_dir, "length.json") print BtLog.status_d["13"] % (length_f) BtIO.writeJson(self.length, length_f, indent=1) # names names_f = join(self.view_dir, "names.json") print BtLog.status_d["13"] % (names_f) BtIO.writeJson(self.names, names_f, indent=1) # cov cov_d = join(self.view_dir, "covs") BtIO.create_dir(directory=cov_d) for cov_lib, cov in self.covs.items(): cov_f = join(cov_d, "%s.json" % cov_lib) print BtLog.status_d["13"] % (cov_f) BtIO.writeJson(cov, cov_f, indent=1) # tax taxrule_d = join(self.view_dir, "taxrule") BtIO.create_dir(directory=taxrule_d) for taxrule in self.tax: tax_d = join(taxrule_d, taxrule) BtIO.create_dir(directory=tax_d) for rank in self.tax[taxrule]: tax = self.tax[taxrule][rank] rank_f = join(tax_d, "%s.json" % rank) BtIO.writeJson(tax, rank_f, indent=1)
def main(): #main_dir = dirname(__file__) args = docopt(__doc__) fasta_f = args['--infile'] fasta_type = args['--type'] sam_fs = args['--sam'] bam_fs = args['--bam'] cov_fs = args['--cov'] cas_fs = args['--cas'] hit_fs = args['--hitsfile'] prefix = args['--out'] nodesDB_f = args['--db'] names_f = args['--names'] nodes_f = args['--nodes'] taxrules = args['--taxrule'] min_bitscore_diff = float(args['--min_diff']) tax_collision_random = args['--tax_collision_random'] title = args['--title'] # outfile out_f = BtIO.getOutFile("blobDB", prefix, "json") if not (title): title = out_f # coverage if not (fasta_type ) and not bam_fs and not sam_fs and not cov_fs and not cas_fs: BtLog.error('1') cov_libs = [BtCore.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \ [BtCore.CovLibObj('sam' + str(idx), 'sam', lib_f) for idx, lib_f in enumerate(sam_fs)] + \ [BtCore.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)] + \ [BtCore.CovLibObj('cov' + str(idx), 'cov', lib_f) for idx, lib_f in enumerate(cov_fs)] # taxonomy hit_libs = [ BtCore.HitLibObj('tax' + str(idx), 'tax', lib_f) for idx, lib_f in enumerate(hit_fs) ] # Create BlobDB object blobDb = BtCore.BlobDb(title) blobDb.version = blobtools.__version__ # Parse FASTA blobDb.parseFasta(fasta_f, fasta_type) # Parse nodesDB OR names.dmp, nodes.dmp nodesDB_default = join(blobtools.DATADIR, "nodesDB.txt") nodesDB, nodesDB_f = BtIO.parseNodesDB(nodes=nodes_f, names=names_f, nodesDB=nodesDB_f, nodesDBdefault=nodesDB_default) blobDb.nodesDB_f = nodesDB_f # Parse similarity hits if (hit_libs): blobDb.parseHits(hit_libs) blobDb.computeTaxonomy(taxrules, nodesDB, min_bitscore_diff, tax_collision_random) else: print BtLog.warn_d['0'] # Parse coverage blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=None) # Generating BlobDB and writing to file print BtLog.status_d['7'] % out_f BtIO.writeJson(blobDb.dump(), out_f)
def output(self): # meta meta = self.get_meta() meta_f = join(self.view_dir, "meta.json") BtIO.writeJson(meta, meta_f, indent=2) # gc gc_f = join(self.view_dir, "gc.json") print BtLog.status_d['13'] % (gc_f) BtIO.writeJson(self.gc, gc_f, indent=1) # length length_f = join(self.view_dir, "length.json") print BtLog.status_d['13'] % (length_f) BtIO.writeJson(self.length, length_f, indent=1) # names names_f = join(self.view_dir, "names.json") print BtLog.status_d['13'] % (names_f) BtIO.writeJson(self.names, names_f, indent=1) # cov cov_d = join(self.view_dir, "covs") BtIO.create_dir(directory=cov_d) for cov_lib, cov in self.covs.items(): cov_f = join(cov_d, "%s.json" % cov_lib) print BtLog.status_d['13'] % (cov_f) BtIO.writeJson(cov, cov_f, indent=1) # tax taxrule_d = join(self.view_dir, "taxrule") BtIO.create_dir(directory=taxrule_d) for taxrule in self.tax: tax_d = join(taxrule_d, taxrule) BtIO.create_dir(directory=tax_d) for rank in self.tax[taxrule]: tax = self.tax[taxrule][rank] rank_f = join(tax_d, "%s.json" % rank) BtIO.writeJson(tax, rank_f, indent=1)